How to get the species abundance in metagenomic data sequenced by PacBio/Nanopore?

Question

[u9313025]

Hello Experts,

I am working with some microbial metagenomic data. As the third-generation sequencer be come more famous. I wonder if there is any method to get the species abundance in metagenomic data sequenced by PacBio or Nanopore ? In short-read platform, I am using bwa to map the reads to the contigs and count the read depth as raw abundance. But how it will be in long read platform? Can I use the same strategy to get the abundance? (ex: minimap2) or there is a better way to do it.

Thank you.

[Devika]

Any answer to this query? Pls help

Answer 1

[colindaven]

I wrote an alignment based metagenomics workflow to do this at https://github.com/MHH-RCUG/nf_wochenende - but what are you trying to quantify (you'll need an appropriate reference fasta) ?

Also doesn't Nanopores WIMP workflow allow you to do this ? https://github.com/epi2me-labs/wf-metagenomics

There are more tools if you google a bit.